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-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex100
1 files changed, 51 insertions, 49 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index c2a73256dc8..58282621d33 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format manual by Akira Yamaji 2017.01.03
+% Molecular Coding Format manual by Akira Yamaji 2017.01.09
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
%%%%\usepackage{graphicx}
@@ -78,7 +78,7 @@
\newpage
\section{Introduction}
Molecular Coding Format(MCF) is new linear notation
- represent chemical structure diagrams.
+represent chemical structure diagrams.
This 'Coding' is named from coding(programing) technique
like adressing,grouping,macro,etc.
There are no Meta language commands in MCF.
@@ -173,22 +173,25 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\subsubsection{Double,triple}
\begin{verbatim}
a~type : ~~type,a
- dm : double middle
- dl : double left side
- dr : double right side
- tm : triple
- <30,!~dm,!~dl,!~dr,!~tm
+ dm : double middle
+ dl : double left side
+ dr : double right side
+ db : double left or right side
+ tm : triple
+ !! : !~db / !!! : !~tm
+
+ <30,!~dm,!,!~dl,!,!~dr,!~db,!~db,!,!~tm
+ <30,!~dm,!,!~dl,!,!~dr,!! ,!! ,!,!!!
\end{verbatim}
\MCFstructure
\vspace{-3mm}%
\begin{verbatim}
- dm dl dr tm
+ dm dl dr db db tm
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Wedge}
\begin{verbatim}
- wf : wedge forward
- wb : wedge backward
+ wf : wedge forward / wb : wedge backward
zf : wedge dotted
zb : wedge dotted backward
@@ -202,8 +205,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
%-----------------------------------------------------------------------------
\subsubsection{Vector}
\begin{verbatim}
- vf : vector forward
- vb : vector backward
+ vf:vector forward / vb:vector backward
<30,!~vf,!,!~vb
\end{verbatim}
@@ -254,7 +256,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
bd_ : broad over line
<-30,!8,!,60,90`8,
- @(2~si_,4~wf_,6~wb_,8~bd_)/Me`2
+ @(2~si_,4~wf_,6~wb_,8~bd_)/_`2
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -428,9 +430,9 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
<30,!,/Me,!,/Et,!3,/Pr,!,/iPr,
!3,/tBu,!,/Ph^-30,!
- ** Me:methyl Et:ethyl(!)
- Pr:propyl(!2) iPr:isopropyl
- tBu:tertial buthyl(!3) Ph:phenyl
+ ** Me:methyl(/_) Et:ethyl(/!)
+ Pr:propyl(/!2) iPr:isopropyl
+ tBu:tertial buthyl Ph:phenyl
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -455,14 +457,14 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
` : change length
> : change enviroment
- <30,``1,!,/Me~zf`2^30,
+ <30,``1,!,/_~zf`2^30,
!2,*/!2>lr,!2,*/!2>rl,!)
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
\subsubsection{Add substituent}
\begin{verbatim}
- <-30,!17,2:/Me,4:/!,6:/!2,
+ <-30,!17,2:/_,4:/!,6:/!2,
10:/iPr,14:/tBu,16:/Ph^-60
\end{verbatim}
\MCFstructure
@@ -472,7 +474,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
~,^,` : change type,angle,length
<-30,!6,
- @(2~wf,4~zf,6^-30)/Me
+ @(2~wf,4~zf,6^-30)/_
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -481,7 +483,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
^,`,> : change angle,length,environment
<30,!7`1,
- 3:/*Me`2^30,5:*/!2>lr,7:*/!2>rl
+ 3:/*_`2^30,5:*/!2>lr,7:*/!2>rl
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -567,7 +569,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\begin{verbatim}
iBuOH : user defined substructure
- iBuOH:='(!,/Me,!,OH)
+ iBuOH:='(!,/_,!,OH)
MCf(<30,?6,@(4,6)/iBuOH)
\end{verbatim}
\MCFstructure
@@ -576,7 +578,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\begin{verbatim}
Insert user defined substructure
- <30,!3,/'(!,/Me,!,OH),!3
+ <30,!3,/'(!,/_,!,OH),!3
\end{verbatim}
\MCFstructure
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -590,7 +592,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
font_wd#:=30mm#; %<==font width
font_ht#:=20mm#; %<==font height
MCf(<30,?6,-4=?5,$(3,8)dl,@(2,6,7,9)N,
- @(2,6,9)/Me,@(1,5)//O) endfont
+ @(2,6,9)/_,@(1,5)//O) endfont
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -1010,8 +1012,8 @@ cFM:calculated molecular formula
\begin{verbatim}
beginfont("EN:Tocopherol","CAS:59-02-9")
MCf(<30,Ph,3=?6,
- 7:O,@(1,2,5)/Me,8:/*Me^60,6:/OH,
- 8\,|,!12,@(4,8)/*Me,12:/Me)
+ 7:O,@(1,2,5)/_,8:/*_^60,6:/OH,
+ 8\,|,!12,@(4,8)/*_,12:/_)
endfont
%% Output to mcf_man_soc-info.aux %%
@@ -1029,7 +1031,7 @@ aux_delimiter:="/";
beginfont("EN:Ampicillin","CAS:69-53-4")
MCf(<45,?4,2:N,2=?5,-1:S,
@(3^45,4^-45)/*H,1://O^15,
- 5:/*COOH^-18,@(6^35,6^-35)/Me,
+ 5:/*COOH^-18,@(6^35,6^-35)/_,
4*\^75,NH,!,//O,!,/*NH2,!,Ph)
endfont
beginfont(......)
@@ -1052,9 +1054,9 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
sw_auxfix:=1; auxtag_out;
beginfont("EN:Cholesterol","NO:1")
MCf(<30,?6,$(-4,-2)?6,-4=?5,7=dl,
- 1:*/OH,@(4,12)*/Me^60,9:*/H^60,
+ 1:*/OH,@(4,12)*/_^60,9:*/H^60,
10:/*H^180,11:/*H^-60,17:/*H^-54,
- -1\^18,/*Me,-60,!3,/Me,!)
+ -1\^18,/*_,-60,!3,/_,!)
endfont
beginfont(......)
...........
@@ -1084,7 +1086,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
<30,?6,$(-3,-4)?6,-5=?3,
-2=wf,-1=wb,6=?5,-4=?6,-5=wf,
@(13,15,17,20)O,@(3,12,21)//O,
- @(4~wf^60,8~zf^60,18^35,18^-35)/Me,
+ @(4~wf^60,8~zf^60,18^35,18^-35)/_,
@(1^60,5^180,16^60)/*H,
14\*,|,?5,$(1,4)dl,3:O
\end{verbatim}
@@ -1125,8 +1127,8 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
8*,160`1.3,&3,
13=dl,6=wf,8=wb,
5*,40~zf`1,O,60,//O^180,&14~zb,
- 2:/COOH,7://Me,13:*/OH,8:/*OH,
- 14:*/Me,@(1^60,4^60)*/H
+ 2:/COOH,7://_,13:*/OH,8:/*OH,
+ 14:*/_,@(1^60,4^60)*/H
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -1135,7 +1137,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
<30,Ph,3=Ph,7:N,6:/O!,
10\,*/OH,/H~zf^-60,!,
|,?6,2:N,1:*/H^60,
- 4*\,!~dr,
+ 4*\,!!,
2*,165~zf,60,&5~zb
\end{verbatim}
\MCFstructure
@@ -1144,7 +1146,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\begin{verbatim}
<-30,O,!,//O,!,!,Ph,
#1\~zb^-120,
- |,?7,6*\^190`1.02,N,/Me,&3~wb,
+ |,?7,6*\^190`1.02,N,/_,&3~wb,
#3\~wv,!,OH
\end{verbatim}
\MCFstructure
@@ -1154,15 +1156,15 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
<-60,?5,$(-3,-2,-3,-4)?6,
$(7,9,-2,-4)dl,$(3,17)dr,
@(2,13,16)O,10://O,@(11^-60,12^60)*/H,
- @(-2,-3)/O!,1*\,/Me,!~dl
+ @(-2,-3)/O!,1*\,/_,!!
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
\subsection{Pyrethrin I}
\begin{verbatim}
- <30,?3,@(3^35~wf,3^-35~zf)/Me,
- 1*\,!~dl,iPr,2\*,//O,!,O,-36~zb,|,
- ?5,-2=d,-1:/Me,-3://O,-2\,!4,$(-1,-3)dl
+ <30,?3,@(3^35~wf,3^-35~zf)/_,
+ 1*\,!!,iPr,2\*,//O,!,O,-36~zb,|,
+ ?5,-2=d,-1:/_,-3://O,-2\,!4,$(-1,-3)dl
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -1178,8 +1180,8 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\begin{verbatim}
?6,5=d,3*,{,``1,36,45,45,45,45,},&#5,
-4=?6,-4=?4,-1=wb,-3=wf,-1:O,||,
- @(4^35,4^-35,6)/Me,@(3^-60,15)*/OH,
- 8:/*H^-60,9:*/Me^60,10://O,
+ @(4^35,4^-35,6)/_,@(3^-60,15)*/OH,
+ 8:/*H^-60,9:*/_^60,10://O,
1\,O,!,//O,!,*/OH,!,/Ph,
60~wf,NH,-60,//O,60,Ph,
7\*,O,-45,//O,60,Ph,11*\,O,-60,//O,60,
@@ -1187,7 +1189,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\onecolumn%
+\onecolumn
\section{Example to use mcf2graph}
\subsection{Molecular definition file}
\begin{verbatim}
@@ -1205,15 +1207,15 @@ outputtemplate:="%j-%3c.png"; >
beginfont("NO:1","EN:Ampicillin") > begin font(information)
MCf(<45,?4,2:N,2=?5,-1:S, > begin MCF (1)
@(3^45,4^-45)/*H,1://O^15,5:/*COOH^-18, >
- @(6^35,6^-35)/Me, >
+ @(6^35,6^-35)/_, >
4\^75,NH,!,//O,!,/*NH,!,Ph) > end MCF
endfont > end font
%------------------------------------------------------------------------
beginfont("NO:2","EN:Cholesterol") > begin font(information)
MCf(<30,?6,$(-4,-2)?6,-4=?5,7=dl, > begin MCF (2)
- 1:*/OH,@(4,12)*/Me^60,9:*/H^60, >
+ 1:*/OH,@(4,12)*/_^60,9:*/H^60, >
10:/*H^180,@(11,-1)/*H^-60, >
- -1\^17,/*Me,!4,/Me,!) > end MCF
+ -1\^17,/*_,!4,/_,!) > end MCF
endfont > end font
%------------------------------------------------------------------------
bye
@@ -1391,7 +1393,7 @@ M END
?6,$(-3,-4)?6,
-5=?3,-2=wf,-1=wb,6=?5,-4=?6,-5=wf,
@(13,15,17,20)O,@(3,12,21)//O,
- @(4~wf^60,8~zf^60,18^35,18^-35)/Me,
+ @(4~wf^60,8~zf^60,18^35,18^-35)/_,
@(1^60,5^180,16^60)/*H,
14\*,|,?5,$(1,4)dl,3:O
)
@@ -1402,10 +1404,10 @@ M END
font_wd:=80mm; font_ht:=50mm;
beginfont("NO:3","EN:beta-carotene","MW:536.87")
MCf(<30,
- ?6,3=dl,@(3,5^35,5^-35)/Me,
+ ?6,3=dl,@(3,5^35,5^-35)/_,
4\,|,!18,$(1,3,5,7,9,11,13,15,17)dr,
- @(3,7,12,16)/Me,
- |,?6,6=dl,@(6,2^35,2^-35)/Me
+ @(3,7,12,16)/_,
+ |,?6,6=dl,@(6,2^35,2^-35)/_
)
endfont
\end{mplibcode}\\
@@ -1416,8 +1418,8 @@ M END
MCf(<18,?5,3=?7,5=?6[12],
8*,160`1.3,&3,13=dl,6=wf,8=wb,
5*,40~zf`1,O,60,//O^180,&14~zb,
- 2:/COOH,7://Me,13:*/OH,8:/*OH,
- 14:*/Me,@(1^60,4^60)*/H
+ 2:/COOH,7://_,13:*/OH,8:/*OH,
+ 14:*/_,@(1^60,4^60)*/H
)
endfont;
\end{mplibcode}\\
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-04 19:26:21 +0000